Cystic fibrosis (CF) is the most common life-shortening genetic disorder in the U.S. Much of the morbidity and mortality in CF is caused by the bacterium Pseudomonas aeruginosa. While some strains of P. aeruginosa are eradicated from the airways of CF patients, others persist and ultimately lead to chronic infections. Once P. aeruginosa infection establishes chronicity, the bacterium cannot be cleared with antibiotics even if it is sensitive when tested ex vivo and exposed to prolonged courses of intravenous antibiotics. The net result is a slowly progressive deterioration of lung function that frequently culminates in death or lung transplantation. Given the severe clinical consequences, new approaches are needed for identifying strains at high risk for causing chronic infections. Which bacterial factors account for the differential persistence of P. aeruginosa in CF airways? Approximately 15% of the P. aeruginosa genome varies from strain to strain. These genes, which confer strain-specific traits, are together referred to as the accessory genome. We hypothesize that the presence or absence of specific accessory genes in some P. aeruginosa strains accounts for their ability to resist eradication and progress to chronic infection in CF. T test our hypothesis, we will utilize unique resources generated by the Early Pseudomonas Infection Control (EPIC) Clinical Trial and Observational Study, which consist of 249 patients from multiple sites followed over a median of almost seven years since initiation of the trial. We propose to use the EPIC cohort to test our hypothesis by completing the following specific aims: (1) In children with CF newly infected with P. aeruginosa, we will identify accessory genes that distinguish isolates that were subsequently eradicated from those that persisted. (2) In children with CF intermittently infected with P. aeruginosa, we will identify accessory genes that distinguish isolates that caused progression to chronic infection from those that did not.